October 29, 2010

Another theory about Neandertal-modern interbreeding

Jean M points me to a paper about the theory of Neandertal introgression into the modern human gene pool that I had overlooked.

The paper echoes many of my criticisms about the theory which I expressed here and here.

The authors put it quite succinctly what was expected of the Neandertal genome by the two competing theories (Out-of-Africa vs. multi-regional) that stand on opposite ends of the spectrum:

There are two predominant models of modern human origins: multiregional evolution and recent African replacement. Multiregional evolution posits that the evolution of contemporary peoples occurred around the globe, with archaic populations such as the Neandertals contributing locally in their geographic regions [4]. This model predicts that Neandertals will share significant genetic variation with Europeans to the exclusion of other populations. Recent African replacement suggests that contemporary humans owe their heritage to a small African population that spread around the world replacing archaic populations with little to no interbreeding [5]. This model predicts that Neandertals will be equally distantly related to all contemporary human populations.

The surprising find about the Neandertal genome is that they were more closely related to Eurasians than to Africans (Yoruba and San): this conflicts with both models. The authors of the original study saw two ways out of this:

First, that humans absorbed Neandertal genes in the Levant that somehow managed to get distributed evenly across Eurasia, to the extent that a Papuan is as close to Neandertals as a European is, even though there is no hint of Neandertal presence in Papua or thousands of km close to it.

Second, that there was African population structure, and that Neandertals and modern humans formed a clade with respect to other African hominids. The breakdown of this structure drove some Africans away from Neandertals, rather than Neandertal admixture in Eurasians driving them towards Neandertals.

The authors of the current paper propose that:

We propose a third alternative. The paleontological and archaeological records suggest that modern humans and Neandertals overlapped in the Eastern Mediterranean region around 100 thousand years ago during a time when the African faunal zone extended temporarily into the Middle East. The range of modern humans then likely contracted back into Africa, severing contact with Neandertals, before finally expanding their range out of Africa around 50 thousand years ago [11]. Admixture may not have been possible during this time because a southern route out of Africa through the Arabian peninsula [12] would not have put the populations in contact. Any admixture would have occurred prior to the expansion of modern humans out of Africa between East Africans and Neandertals (Figure 1C). If this is correct, Neandertal genes will be found at low frequency in East Africans and perhaps others. These low-frequency Neandertal genes may then have been pushed to high frequency or fixation in the out of Africa populations through the iterated founder effect associated with range expansions [13].

The authors call (like I did) for sampling East Africans for evidence of "Neandertal genes".

Of course East African-Neandertal admixture prior to the Eurasian expansion would have the desired effect, the same as my favored model of deep African population structure.

But, a new curveball was thrown our way by the discovery of 100ky anatomically modern humans in south China. The third alternative seems less plausible now: it would be possible to think of modern (Neandertal-admixed) humans retreating back to east Africa after 100ky due to a retreat of African fauna from the Middle East when we didn't know about the Chinese modern Homo sapiens. But, now, we have to conclude that there were modern humans living between Israel and south China 100ky ago, and any idea of retreat becomes implausible.

Thus, I still believe that the 2nd scenario (deep African population structure + common Neandertal-sapiens ancestor in East Africa) is more plausible.

Nonetheless I, like the authors, have arrived -for different reasons- at the same conclusion: east Africans need to be sampled for Neandertal genes.

If humans admixed with Neandertals in Eurasia, then we expect East Africans to have Neandertal genes in proportion to their Eurasian admixture. Let's say 4% Neandertal genes and 10% Eurasian admixture in a particular east African population. Then, we expect about 0.4% Neandertal genes in this population. If we find much more, then there will be something wrong with the theory of "Neandertal admixture in Eurasia".

Current Biology Volume 20, Issue 12, 22 June 2010, Pages R517-R519

Neandertal Genome: The Ins and Outs of African Genetic Diversity

Jason A. Hodgsona, Christina M. Bergeya and Todd R. Disotell

Summary

Analysis of the Neandertal genome indicates gene flow between Neandertals and modern humans of Eurasia but not Africa. This surprising result is difficult to reconcile with current models of human origins and might have to do with insufficient African sampling.

Why do you expect neanderthal DNA presence to be proportional to neanderthal ancestry rather than adaptive value of said dna?That is, could it not be that only the genes that proved to be useful staid in the genome, and they ere the same for every population?

There are mtDNA and Y-DNA sites that are different strictly between Africans and non-Africans (Papuans or Amerindians alike). Why are those non-African alleles not considered "Neanderthal"? The issue here seems to be not whether East Africans have Neanderthal genes or not, but whether non-African alleles are actually older than African alleles because attested in Neanderthals and whether African alleles, although technically identical with those found in chimp sequences are in fact homoplastic. So, say, it's not T (African, chimp) > C (non-African), but T (chimp) > C (Neanderthal, non-African) > T (African).

"In mt-DNA and y-DNA I would say: because it does not get re-shuffled, and Africa has the oldest lineages: i.e., haplogroups that share the least among the least common denominator."

In this case, they are most likely derived and geographically most removed from the homeland, as the oldest haplogroup that stayed behind will share the most among the most common denominators. Look at Rosenberg 2002 or Underhill and Kivisild 2007 and you'll see the clear split in K cluster analysis between the least derived Amerindians and the most derived Africans.

I have yet to see a convincing argument for admixture that addresses the likelihood of its rival hypothesis - genetic drift. Though Europeans might be expected to have this admixture with Neandertals, it does not explain that same similarity in Asians who had no more ability to have contact with Neanderthals than Africans.

What Asians and Europeans have in common is adapting to a colder climate through genetic drift, just as the homo erectus had to adapt to become a neanderthal.

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